Resources & Tools

CultureBotAI develops and maintains various computational resources, databases, and tools for the microbial research community.

🧬 kg-microbe: Microbial Knowledge Graph

Overview

kg-microbe is our flagship resource - a comprehensive knowledge graph that integrates diverse microbial data sources to enable AI-driven insights and predictions.

📄 Read the Preprint - bioRxiv publication detailing kg-microbe development and applications.

📋 METPO Ontology Integration

The Microbial Ecology and Taxonomy Phenotypic Ontology (METPO) plays a crucial role in kg-microbe by providing standardized terminology for microbial phenotypes and ecological characteristics.

Key Benefits:

  • Knowledge Organization - METPO terms provide semantic structure to organize diverse microbial data within the kg-microbe knowledge graph
  • Text Extraction - Standardized ontology terms power automated literature mining and text extraction processes
  • Semantic Consistency - Ensures consistent representation of microbial characteristics across different data sources

Links:

Key Features

  • Multi-source integration from major biological databases
  • Semantic consistency through ontology-driven organization
  • Machine-readable formats (RDF, Neo4j, JSON-LD)
  • Regular updates with automated data refresh pipelines
  • API access for programmatic data retrieval

Data Sources

kg-microbe integrates data from:

  • NCBI Taxonomy - Microbial taxonomy and phylogeny
  • UniProt - Protein sequences and functional annotations
  • GO (Gene Ontology) - Functional gene classifications
  • Environmental ontologies - Habitat and growth condition data
  • Literature sources - Manually curated cultivation data

Applications

  • Growth condition prediction for uncultured organisms
  • Taxonomic relationship exploration and phylogenetic analysis
  • Literature mining for cultivation protocols
  • Cross-organism comparison of growth preferences

Getting Started

# Clone the repository
git clone https://github.com/Knowledge-Graph-Hub/kg-microbe.git

# Install dependencies
cd kg-microbe
pip install -r requirements.txt

# Build latest knowledge graph
kg download
kg transform
kg merge

🔧 Computational Tools

CultureBot Predictor

AI-powered tool for predicting optimal growth conditions for target microorganisms.

Features:

  • Machine learning models trained on kg-microbe data
  • Growth condition recommendations
  • Media composition suggestions
  • Confidence scoring for predictions

📊 Datasets

Curated Cultivation Database

Curated collection of cultivation protocols for diverse microorganisms based on reference sources and literature.

Contents:

  • Growth media compositions
  • Environmental conditions (temperature, pH, atmosphere)
  • Cultivation methods and protocols
  • Literature references

Environmental Metadata Collection

Comprehensive dataset linking microorganisms to their natural habitats and environmental conditions.

🌐 Related Organizations & Resources

Academic & Research Institutions

  • ABPDU - Advanced Biofuels and Bioproducts Process Development Unit
  • BacDive - Bacterial Diversity Metadatabase
  • Cultivarium - Global microbial cultivation platform
  • JBEI - Joint BioEnergy Institute
  • JGI GOLD - Genomes Online Database
  • KBase - Systems Biology Knowledgebase
  • NMDC - National Microbiome Data Collaborative
  • Palsson Lab - UC San Diego Systems Biology Research Group

Commercial Organizations

  • Biolog - Microbial identification and characterization systems
  • Isolation Bio - Microbial isolation and cultivation technology

📚 Documentation & Tutorials

API Documentation

Comprehensive documentation for programmatic access to kg-microbe and related tools:

  • Neo4j graph database interface
  • Python SDK usage examples
  • Data schema specifications

Tutorials

Coming soon!

Example Notebooks

Jupyter notebooks demonstrating practical applications:

  • Growth condition prediction workflows
  • Literature mining pipelines
  • Data visualization examples

🔗 Data Access & APIs

Direct Downloads

  • Knowledge Graph Dumps - Complete RDF/TTL files
  • Processed Datasets - CSV/JSON formatted data tables
  • Ontology Files - OWL/RDF ontology definitions

API Endpoints

Coming soon

Query Interfaces

Coming soon

📦 Software Packages

Python Packages

Coming soon

🤝 Community & Collaboration

Contributing

We welcome contributions from the research community:

  • Data contributions - Share cultivation protocols and growth data
  • Software development - Contribute to open source tools
  • Literature curation - Help extract cultivation data from papers
  • Validation - Test predictions against experimental results

Discussion Forums

  • GitHub Discussions - Technical questions and feature requests
  • Slack Community - Real-time collaboration and support
  • Monthly Webinars - Updates and community presentations

Citation

If you use kg-microbe or other CultureBotAI resources in your research, please cite:

Santangelo, B.E., Hegde, H., Caufield, J.H., Reese, J., Kliegr, T., Hunter, L.E., 
Lozupone, C.A., Mungall, C.J., Joachimiak, M.P. (2025). KG-Microbe - Building 
Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences. 
bioRxiv. https://doi.org/10.1101/2025.02.24.639989

Support & Contact

For technical support, collaboration inquiries, or questions about our resources: